projektAI/venv/Lib/site-packages/sklearn/ensemble/_stacking.py

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2021-06-06 22:13:05 +02:00
"""Stacking classifier and regressor."""
# Authors: Guillaume Lemaitre <g.lemaitre58@gmail.com>
# License: BSD 3 clause
from abc import ABCMeta, abstractmethod
from copy import deepcopy
import numpy as np
from joblib import Parallel
import scipy.sparse as sparse
from ..base import clone
from ..base import ClassifierMixin, RegressorMixin, TransformerMixin
from ..base import is_classifier, is_regressor
from ..exceptions import NotFittedError
from ..utils._estimator_html_repr import _VisualBlock
from ._base import _fit_single_estimator
from ._base import _BaseHeterogeneousEnsemble
from ..linear_model import LogisticRegression
from ..linear_model import RidgeCV
from ..model_selection import cross_val_predict
from ..model_selection import check_cv
from ..preprocessing import LabelEncoder
from ..utils import Bunch
from ..utils.metaestimators import if_delegate_has_method
from ..utils.multiclass import check_classification_targets
from ..utils.validation import check_is_fitted
from ..utils.validation import column_or_1d
from ..utils.validation import _deprecate_positional_args
from ..utils.fixes import delayed
class _BaseStacking(TransformerMixin, _BaseHeterogeneousEnsemble,
metaclass=ABCMeta):
"""Base class for stacking method."""
@abstractmethod
def __init__(self, estimators, final_estimator=None, *, cv=None,
stack_method='auto', n_jobs=None, verbose=0,
passthrough=False):
super().__init__(estimators=estimators)
self.final_estimator = final_estimator
self.cv = cv
self.stack_method = stack_method
self.n_jobs = n_jobs
self.verbose = verbose
self.passthrough = passthrough
def _clone_final_estimator(self, default):
if self.final_estimator is not None:
self.final_estimator_ = clone(self.final_estimator)
else:
self.final_estimator_ = clone(default)
def _concatenate_predictions(self, X, predictions):
"""Concatenate the predictions of each first layer learner and
possibly the input dataset `X`.
If `X` is sparse and `self.passthrough` is False, the output of
`transform` will be dense (the predictions). If `X` is sparse
and `self.passthrough` is True, the output of `transform` will
be sparse.
This helper is in charge of ensuring the predictions are 2D arrays and
it will drop one of the probability column when using probabilities
in the binary case. Indeed, the p(y|c=0) = 1 - p(y|c=1)
"""
X_meta = []
for est_idx, preds in enumerate(predictions):
# case where the the estimator returned a 1D array
if preds.ndim == 1:
X_meta.append(preds.reshape(-1, 1))
else:
if (self.stack_method_[est_idx] == 'predict_proba' and
len(self.classes_) == 2):
# Remove the first column when using probabilities in
# binary classification because both features are perfectly
# collinear.
X_meta.append(preds[:, 1:])
else:
X_meta.append(preds)
if self.passthrough:
X_meta.append(X)
if sparse.issparse(X):
return sparse.hstack(X_meta, format=X.format)
return np.hstack(X_meta)
@staticmethod
def _method_name(name, estimator, method):
if estimator == 'drop':
return None
if method == 'auto':
if getattr(estimator, 'predict_proba', None):
return 'predict_proba'
elif getattr(estimator, 'decision_function', None):
return 'decision_function'
else:
return 'predict'
else:
if not hasattr(estimator, method):
raise ValueError('Underlying estimator {} does not implement '
'the method {}.'.format(name, method))
return method
def fit(self, X, y, sample_weight=None):
"""Fit the estimators.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : array-like of shape (n_samples,)
Target values.
sample_weight : array-like of shape (n_samples,) or default=None
Sample weights. If None, then samples are equally weighted.
Note that this is supported only if all underlying estimators
support sample weights.
.. versionchanged:: 0.23
when not None, `sample_weight` is passed to all underlying
estimators
Returns
-------
self : object
"""
# all_estimators contains all estimators, the one to be fitted and the
# 'drop' string.
names, all_estimators = self._validate_estimators()
self._validate_final_estimator()
stack_method = [self.stack_method] * len(all_estimators)
# Fit the base estimators on the whole training data. Those
# base estimators will be used in transform, predict, and
# predict_proba. They are exposed publicly.
self.estimators_ = Parallel(n_jobs=self.n_jobs)(
delayed(_fit_single_estimator)(clone(est), X, y, sample_weight)
for est in all_estimators if est != 'drop'
)
self.named_estimators_ = Bunch()
est_fitted_idx = 0
for name_est, org_est in zip(names, all_estimators):
if org_est != 'drop':
self.named_estimators_[name_est] = self.estimators_[
est_fitted_idx]
est_fitted_idx += 1
else:
self.named_estimators_[name_est] = 'drop'
# To train the meta-classifier using the most data as possible, we use
# a cross-validation to obtain the output of the stacked estimators.
# To ensure that the data provided to each estimator are the same, we
# need to set the random state of the cv if there is one and we need to
# take a copy.
cv = check_cv(self.cv, y=y, classifier=is_classifier(self))
if hasattr(cv, 'random_state') and cv.random_state is None:
cv.random_state = np.random.RandomState()
self.stack_method_ = [
self._method_name(name, est, meth)
for name, est, meth in zip(names, all_estimators, stack_method)
]
fit_params = ({"sample_weight": sample_weight}
if sample_weight is not None
else None)
predictions = Parallel(n_jobs=self.n_jobs)(
delayed(cross_val_predict)(clone(est), X, y, cv=deepcopy(cv),
method=meth, n_jobs=self.n_jobs,
fit_params=fit_params,
verbose=self.verbose)
for est, meth in zip(all_estimators, self.stack_method_)
if est != 'drop'
)
# Only not None or not 'drop' estimators will be used in transform.
# Remove the None from the method as well.
self.stack_method_ = [
meth for (meth, est) in zip(self.stack_method_, all_estimators)
if est != 'drop'
]
X_meta = self._concatenate_predictions(X, predictions)
_fit_single_estimator(self.final_estimator_, X_meta, y,
sample_weight=sample_weight)
return self
@property
def n_features_in_(self):
"""Number of features seen during :term:`fit`."""
try:
check_is_fitted(self)
except NotFittedError as nfe:
raise AttributeError(
f"{self.__class__.__name__} object has no attribute "
f"n_features_in_") from nfe
return self.estimators_[0].n_features_in_
def _transform(self, X):
"""Concatenate and return the predictions of the estimators."""
check_is_fitted(self)
predictions = [
getattr(est, meth)(X)
for est, meth in zip(self.estimators_, self.stack_method_)
if est != 'drop'
]
return self._concatenate_predictions(X, predictions)
@if_delegate_has_method(delegate='final_estimator_')
def predict(self, X, **predict_params):
"""Predict target for X.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
**predict_params : dict of str -> obj
Parameters to the `predict` called by the `final_estimator`. Note
that this may be used to return uncertainties from some estimators
with `return_std` or `return_cov`. Be aware that it will only
accounts for uncertainty in the final estimator.
Returns
-------
y_pred : ndarray of shape (n_samples,) or (n_samples, n_output)
Predicted targets.
"""
check_is_fitted(self)
return self.final_estimator_.predict(
self.transform(X), **predict_params
)
def _sk_visual_block_(self, final_estimator):
names, estimators = zip(*self.estimators)
parallel = _VisualBlock('parallel', estimators, names=names,
dash_wrapped=False)
serial = _VisualBlock('serial', (parallel, final_estimator),
dash_wrapped=False)
return _VisualBlock('serial', [serial])
class StackingClassifier(ClassifierMixin, _BaseStacking):
"""Stack of estimators with a final classifier.
Stacked generalization consists in stacking the output of individual
estimator and use a classifier to compute the final prediction. Stacking
allows to use the strength of each individual estimator by using their
output as input of a final estimator.
Note that `estimators_` are fitted on the full `X` while `final_estimator_`
is trained using cross-validated predictions of the base estimators using
`cross_val_predict`.
Read more in the :ref:`User Guide <stacking>`.
.. versionadded:: 0.22
Parameters
----------
estimators : list of (str, estimator)
Base estimators which will be stacked together. Each element of the
list is defined as a tuple of string (i.e. name) and an estimator
instance. An estimator can be set to 'drop' using `set_params`.
final_estimator : estimator, default=None
A classifier which will be used to combine the base estimators.
The default classifier is a
:class:`~sklearn.linear_model.LogisticRegression`.
cv : int, cross-validation generator or an iterable, default=None
Determines the cross-validation splitting strategy used in
`cross_val_predict` to train `final_estimator`. Possible inputs for
cv are:
* None, to use the default 5-fold cross validation,
* integer, to specify the number of folds in a (Stratified) KFold,
* An object to be used as a cross-validation generator,
* An iterable yielding train, test splits.
For integer/None inputs, if the estimator is a classifier and y is
either binary or multiclass,
:class:`~sklearn.model_selection.StratifiedKFold` is used.
In all other cases, :class:`~sklearn.model_selection.KFold` is used.
These splitters are instantiated with `shuffle=False` so the splits
will be the same across calls.
Refer :ref:`User Guide <cross_validation>` for the various
cross-validation strategies that can be used here.
.. note::
A larger number of split will provide no benefits if the number
of training samples is large enough. Indeed, the training time
will increase. ``cv`` is not used for model evaluation but for
prediction.
stack_method : {'auto', 'predict_proba', 'decision_function', 'predict'}, \
default='auto'
Methods called for each base estimator. It can be:
* if 'auto', it will try to invoke, for each estimator,
`'predict_proba'`, `'decision_function'` or `'predict'` in that
order.
* otherwise, one of `'predict_proba'`, `'decision_function'` or
`'predict'`. If the method is not implemented by the estimator, it
will raise an error.
n_jobs : int, default=None
The number of jobs to run in parallel all `estimators` `fit`.
`None` means 1 unless in a `joblib.parallel_backend` context. -1 means
using all processors. See Glossary for more details.
passthrough : bool, default=False
When False, only the predictions of estimators will be used as
training data for `final_estimator`. When True, the
`final_estimator` is trained on the predictions as well as the
original training data.
verbose : int, default=0
Verbosity level.
Attributes
----------
classes_ : ndarray of shape (n_classes,)
Class labels.
estimators_ : list of estimators
The elements of the estimators parameter, having been fitted on the
training data. If an estimator has been set to `'drop'`, it
will not appear in `estimators_`.
named_estimators_ : :class:`~sklearn.utils.Bunch`
Attribute to access any fitted sub-estimators by name.
final_estimator_ : estimator
The classifier which predicts given the output of `estimators_`.
stack_method_ : list of str
The method used by each base estimator.
Notes
-----
When `predict_proba` is used by each estimator (i.e. most of the time for
`stack_method='auto'` or specifically for `stack_method='predict_proba'`),
The first column predicted by each estimator will be dropped in the case
of a binary classification problem. Indeed, both feature will be perfectly
collinear.
References
----------
.. [1] Wolpert, David H. "Stacked generalization." Neural networks 5.2
(1992): 241-259.
Examples
--------
>>> from sklearn.datasets import load_iris
>>> from sklearn.ensemble import RandomForestClassifier
>>> from sklearn.svm import LinearSVC
>>> from sklearn.linear_model import LogisticRegression
>>> from sklearn.preprocessing import StandardScaler
>>> from sklearn.pipeline import make_pipeline
>>> from sklearn.ensemble import StackingClassifier
>>> X, y = load_iris(return_X_y=True)
>>> estimators = [
... ('rf', RandomForestClassifier(n_estimators=10, random_state=42)),
... ('svr', make_pipeline(StandardScaler(),
... LinearSVC(random_state=42)))
... ]
>>> clf = StackingClassifier(
... estimators=estimators, final_estimator=LogisticRegression()
... )
>>> from sklearn.model_selection import train_test_split
>>> X_train, X_test, y_train, y_test = train_test_split(
... X, y, stratify=y, random_state=42
... )
>>> clf.fit(X_train, y_train).score(X_test, y_test)
0.9...
"""
@_deprecate_positional_args
def __init__(self, estimators, final_estimator=None, *, cv=None,
stack_method='auto', n_jobs=None, passthrough=False,
verbose=0):
super().__init__(
estimators=estimators,
final_estimator=final_estimator,
cv=cv,
stack_method=stack_method,
n_jobs=n_jobs,
passthrough=passthrough,
verbose=verbose
)
def _validate_final_estimator(self):
self._clone_final_estimator(default=LogisticRegression())
if not is_classifier(self.final_estimator_):
raise ValueError(
"'final_estimator' parameter should be a classifier. Got {}"
.format(self.final_estimator_)
)
def fit(self, X, y, sample_weight=None):
"""Fit the estimators.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : array-like of shape (n_samples,)
Target values.
sample_weight : array-like of shape (n_samples,), default=None
Sample weights. If None, then samples are equally weighted.
Note that this is supported only if all underlying estimators
support sample weights.
Returns
-------
self : object
"""
check_classification_targets(y)
self._le = LabelEncoder().fit(y)
self.classes_ = self._le.classes_
return super().fit(X, self._le.transform(y), sample_weight)
@if_delegate_has_method(delegate='final_estimator_')
def predict(self, X, **predict_params):
"""Predict target for X.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
**predict_params : dict of str -> obj
Parameters to the `predict` called by the `final_estimator`. Note
that this may be used to return uncertainties from some estimators
with `return_std` or `return_cov`. Be aware that it will only
accounts for uncertainty in the final estimator.
Returns
-------
y_pred : ndarray of shape (n_samples,) or (n_samples, n_output)
Predicted targets.
"""
y_pred = super().predict(X, **predict_params)
return self._le.inverse_transform(y_pred)
@if_delegate_has_method(delegate='final_estimator_')
def predict_proba(self, X):
"""Predict class probabilities for X using
`final_estimator_.predict_proba`.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
Returns
-------
probabilities : ndarray of shape (n_samples, n_classes) or \
list of ndarray of shape (n_output,)
The class probabilities of the input samples.
"""
check_is_fitted(self)
return self.final_estimator_.predict_proba(self.transform(X))
@if_delegate_has_method(delegate='final_estimator_')
def decision_function(self, X):
"""Predict decision function for samples in X using
`final_estimator_.decision_function`.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
Returns
-------
decisions : ndarray of shape (n_samples,), (n_samples, n_classes), \
or (n_samples, n_classes * (n_classes-1) / 2)
The decision function computed the final estimator.
"""
check_is_fitted(self)
return self.final_estimator_.decision_function(self.transform(X))
def transform(self, X):
"""Return class labels or probabilities for X for each estimator.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where `n_samples` is the number of samples and
`n_features` is the number of features.
Returns
-------
y_preds : ndarray of shape (n_samples, n_estimators) or \
(n_samples, n_classes * n_estimators)
Prediction outputs for each estimator.
"""
return self._transform(X)
def _sk_visual_block_(self):
# If final_estimator's default changes then this should be
# updated.
if self.final_estimator is None:
final_estimator = LogisticRegression()
else:
final_estimator = self.final_estimator
return super()._sk_visual_block_(final_estimator)
class StackingRegressor(RegressorMixin, _BaseStacking):
"""Stack of estimators with a final regressor.
Stacked generalization consists in stacking the output of individual
estimator and use a regressor to compute the final prediction. Stacking
allows to use the strength of each individual estimator by using their
output as input of a final estimator.
Note that `estimators_` are fitted on the full `X` while `final_estimator_`
is trained using cross-validated predictions of the base estimators using
`cross_val_predict`.
Read more in the :ref:`User Guide <stacking>`.
.. versionadded:: 0.22
Parameters
----------
estimators : list of (str, estimator)
Base estimators which will be stacked together. Each element of the
list is defined as a tuple of string (i.e. name) and an estimator
instance. An estimator can be set to 'drop' using `set_params`.
final_estimator : estimator, default=None
A regressor which will be used to combine the base estimators.
The default regressor is a :class:`~sklearn.linear_model.RidgeCV`.
cv : int, cross-validation generator or an iterable, default=None
Determines the cross-validation splitting strategy used in
`cross_val_predict` to train `final_estimator`. Possible inputs for
cv are:
* None, to use the default 5-fold cross validation,
* integer, to specify the number of folds in a (Stratified) KFold,
* An object to be used as a cross-validation generator,
* An iterable yielding train, test splits.
For integer/None inputs, if the estimator is a classifier and y is
either binary or multiclass,
:class:`~sklearn.model_selection.StratifiedKFold` is used.
In all other cases, :class:`~sklearn.model_selection.KFold` is used.
These splitters are instantiated with `shuffle=False` so the splits
will be the same across calls.
Refer :ref:`User Guide <cross_validation>` for the various
cross-validation strategies that can be used here.
.. note::
A larger number of split will provide no benefits if the number
of training samples is large enough. Indeed, the training time
will increase. ``cv`` is not used for model evaluation but for
prediction.
n_jobs : int, default=None
The number of jobs to run in parallel for `fit` of all `estimators`.
`None` means 1 unless in a `joblib.parallel_backend` context. -1 means
using all processors. See Glossary for more details.
passthrough : bool, default=False
When False, only the predictions of estimators will be used as
training data for `final_estimator`. When True, the
`final_estimator` is trained on the predictions as well as the
original training data.
verbose : int, default=0
Verbosity level.
Attributes
----------
estimators_ : list of estimator
The elements of the estimators parameter, having been fitted on the
training data. If an estimator has been set to `'drop'`, it
will not appear in `estimators_`.
named_estimators_ : :class:`~sklearn.utils.Bunch`
Attribute to access any fitted sub-estimators by name.
final_estimator_ : estimator
The regressor to stacked the base estimators fitted.
References
----------
.. [1] Wolpert, David H. "Stacked generalization." Neural networks 5.2
(1992): 241-259.
Examples
--------
>>> from sklearn.datasets import load_diabetes
>>> from sklearn.linear_model import RidgeCV
>>> from sklearn.svm import LinearSVR
>>> from sklearn.ensemble import RandomForestRegressor
>>> from sklearn.ensemble import StackingRegressor
>>> X, y = load_diabetes(return_X_y=True)
>>> estimators = [
... ('lr', RidgeCV()),
... ('svr', LinearSVR(random_state=42))
... ]
>>> reg = StackingRegressor(
... estimators=estimators,
... final_estimator=RandomForestRegressor(n_estimators=10,
... random_state=42)
... )
>>> from sklearn.model_selection import train_test_split
>>> X_train, X_test, y_train, y_test = train_test_split(
... X, y, random_state=42
... )
>>> reg.fit(X_train, y_train).score(X_test, y_test)
0.3...
"""
@_deprecate_positional_args
def __init__(self, estimators, final_estimator=None, *, cv=None,
n_jobs=None, passthrough=False, verbose=0):
super().__init__(
estimators=estimators,
final_estimator=final_estimator,
cv=cv,
stack_method="predict",
n_jobs=n_jobs,
passthrough=passthrough,
verbose=verbose
)
def _validate_final_estimator(self):
self._clone_final_estimator(default=RidgeCV())
if not is_regressor(self.final_estimator_):
raise ValueError(
"'final_estimator' parameter should be a regressor. Got {}"
.format(self.final_estimator_)
)
def fit(self, X, y, sample_weight=None):
"""Fit the estimators.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
y : array-like of shape (n_samples,)
Target values.
sample_weight : array-like of shape (n_samples,), default=None
Sample weights. If None, then samples are equally weighted.
Note that this is supported only if all underlying estimators
support sample weights.
Returns
-------
self : object
"""
y = column_or_1d(y, warn=True)
return super().fit(X, y, sample_weight)
def transform(self, X):
"""Return the predictions for X for each estimator.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vectors, where `n_samples` is the number of samples and
`n_features` is the number of features.
Returns
-------
y_preds : ndarray of shape (n_samples, n_estimators)
Prediction outputs for each estimator.
"""
return self._transform(X)
def _sk_visual_block_(self):
# If final_estimator's default changes then this should be
# updated.
if self.final_estimator is None:
final_estimator = RidgeCV()
else:
final_estimator = self.final_estimator
return super()._sk_visual_block_(final_estimator)